I think I'm in agreement with the Dans here... Although your ref definitely has an attitude problem!
And I don't think this should ever be a competition. C5's "GM sets puzzle and tries to prevent players solving it" is one (perfectly valid) approach to gaming, but to me, the GM is trying to tell a story with the players, rather than in spite of them. And the same goes for the relationship in the other direction.
And personally, if the ref thinks you're a bad Captain, why not give him the opportunity to prove it for real? Offer to run the game for a couple of sessions, with him in charge of the vessel.
To keep it within the series setting, you could set it up in a similar manner to "Chain of Command" with a replacement captain brought in while your PC does a special mission.
Just a thought...
Jon
"There are worlds out there where the sky is burning, where the sea is asleep and the rivers dream; people made of smoke and cities made of song.
Somewhere there's danger, somewhere there's injustice, and somewhere else the tea is getting cold. Come on, Ace, we've got work to do."
THE DOCTOR, "Survival" (Doctor Who)